After hitting "start application", it disappears from my device manager tree, so I've been re-plugging the USB and holding down SW0 to reload programs. Has anyone come experienced this? Perhaps it would be better to buy an Atmel ICE

So, one goal accomplished. That is to program it within AS7, but, the board still disconnects each time I program it (with the Windows' USB ding-dong sound happening after uploading). Gchapman, you mentioned dfu-programming and avrdude as alternatives. Would these fix this issue? To be honest, it's mostly for convenience just so I don't have to re-plug it in each time, because I'll be using this board a lot these next couple months. Or is using Atmel ICE a better bet?

Edit: I bit the bullet and bought an Atmel ICE, so this is somewhat obsolete now. Thank you for your help though, and to those who helped me blink the LED!

I don't remember having problems using avrdude flip2 to program this board. I just tried today running Win10 1703 and found Atmel's driver doesn't work. I tried to reinstall the driver and got an error in the .inf file. Actually I didn't really know what I was doing. I just pointed Microsoft's driver installer at Atmel's USB_DRIVER folder and turned it loose. I have AS 6.2 installed. That might be the problem with the driver.

It's not a pressing problem though because I seldom use the board. I should be able to program it with my AVR ICE and PDI. And I can also boot up another Windows installation. And I could install a non-DFU bootloader like my quick and dirty AVR911 bootloader. I just keep this board with Atmel's DFU bootloader around for intellectual curiosity.

As is usually the case, this Atmel board doesn't come with a reset button. I fixed that. I have a little board that plugs into the JTAG port. It gives me a reset button and a Steve17 standard PDI connector. I also have a small plugin board that gives me a Steve17 standard USART connector.